Job ID = 6368158 SRX = SRX494842 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:30 prefetch.2.10.7: 1) Downloading 'SRR1198374'... 2020-06-16T00:04:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:06:16 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:06:16 prefetch.2.10.7: 'SRR1198374' is valid 2020-06-16T00:06:16 prefetch.2.10.7: 1) 'SRR1198374' was downloaded successfully Read 7317351 spots for SRR1198374/SRR1198374.sra Written 7317351 spots for SRR1198374/SRR1198374.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:24 7317351 reads; of these: 7317351 (100.00%) were unpaired; of these: 197732 (2.70%) aligned 0 times 4610565 (63.01%) aligned exactly 1 time 2509054 (34.29%) aligned >1 times 97.30% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2928818 / 7119619 = 0.4114 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:10:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:06: 1000000 INFO @ Tue, 16 Jun 2020 09:10:12: 2000000 INFO @ Tue, 16 Jun 2020 09:10:17: 3000000 INFO @ Tue, 16 Jun 2020 09:10:23: 4000000 INFO @ Tue, 16 Jun 2020 09:10:24: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:10:24: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:10:24: #1 total tags in treatment: 4190801 INFO @ Tue, 16 Jun 2020 09:10:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:10:24: #1 tags after filtering in treatment: 4190801 INFO @ Tue, 16 Jun 2020 09:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:25: #2 number of paired peaks: 6111 INFO @ Tue, 16 Jun 2020 09:10:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:25: #2 predicted fragment length is 225 bps INFO @ Tue, 16 Jun 2020 09:10:25: #2 alternative fragment length(s) may be 3,211,225 bps INFO @ Tue, 16 Jun 2020 09:10:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.05_model.r INFO @ Tue, 16 Jun 2020 09:10:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:25: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:10:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:10:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:36: 1000000 INFO @ Tue, 16 Jun 2020 09:10:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:41: 2000000 INFO @ Tue, 16 Jun 2020 09:10:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.05_summits.bed INFO @ Tue, 16 Jun 2020 09:10:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2190 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:46: 3000000 INFO @ Tue, 16 Jun 2020 09:10:51: 4000000 INFO @ Tue, 16 Jun 2020 09:10:52: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:10:52: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:10:52: #1 total tags in treatment: 4190801 INFO @ Tue, 16 Jun 2020 09:10:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:10:52: #1 tags after filtering in treatment: 4190801 INFO @ Tue, 16 Jun 2020 09:10:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:53: #2 number of paired peaks: 6111 INFO @ Tue, 16 Jun 2020 09:10:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:53: #2 predicted fragment length is 225 bps INFO @ Tue, 16 Jun 2020 09:10:53: #2 alternative fragment length(s) may be 3,211,225 bps INFO @ Tue, 16 Jun 2020 09:10:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.10_model.r INFO @ Tue, 16 Jun 2020 09:10:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:11:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:06: 1000000 INFO @ Tue, 16 Jun 2020 09:11:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:12: 2000000 INFO @ Tue, 16 Jun 2020 09:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.10_summits.bed INFO @ Tue, 16 Jun 2020 09:11:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (985 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:18: 3000000 INFO @ Tue, 16 Jun 2020 09:11:23: 4000000 INFO @ Tue, 16 Jun 2020 09:11:24: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:11:24: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:11:24: #1 total tags in treatment: 4190801 INFO @ Tue, 16 Jun 2020 09:11:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:11:24: #1 tags after filtering in treatment: 4190801 INFO @ Tue, 16 Jun 2020 09:11:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:25: #2 number of paired peaks: 6111 INFO @ Tue, 16 Jun 2020 09:11:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:25: #2 predicted fragment length is 225 bps INFO @ Tue, 16 Jun 2020 09:11:25: #2 alternative fragment length(s) may be 3,211,225 bps INFO @ Tue, 16 Jun 2020 09:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.20_model.r INFO @ Tue, 16 Jun 2020 09:11:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494842/SRX494842.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (302 records, 4 fields): 2 millis CompletedMACS2peakCalling